Decoding the Gut Microbiome: An Introduction to Computational Biology

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Course DatesMeeting TimesStatusInstructor(s)CRNRegistration
June 17, 2019 - June 28, 20196/17 - 6/28M-F 8:30A-11:20AOpenKellyanne Duncan

Course Description

In this course, students will learn the basics of coding and how we use it to study the gut microbiome. Researchers have only recently realized the importance of the gut microbiome to many different aspects of human health, but often the data produced from these studies are too large and complex to understand. Only with coding and bioinformatics can we transform these large datasets into understandable and meaningful data. The skills learned in this course are applicable to every STEM field as the ability to interpret data from large datasets becomes increasingly important.

The focus of this course is to learn the computational techniques researchers use to evaluate the composition of microbial communities, specifically within the gut microbiome. To achieve this, students will learn about different types of sequencing and how it is used to identify different microbes and their functions. Students will also learn how sequencing data, containing an insurmountable amount of raw values, can be processed through various analyses to create understandable data. To do this, students will learn what the command line is and the basics of how to operate within it, as well as using it to code various analyses microbiologists use. Learning how to code can be daunting, which is why the basics will be broken down to provide a solid foundation of understanding, and students will engage with the material by completing assignments to reinforce topics covered in class as well as participate in online discussions with their peers. Students will also participate in a group project where they will take raw sequencing data and determine what that data tells us about which microbes are there. This course provides a useful skill for better understanding microbial communities as we continue to learn about the influence of the gut microbiome on host health as well as a foundation of knowledge on how large datasets are handled, applicable to a variety of fields.

By the end of the course, students will:
• Be comfortable using the command line to communicate with their computer
• Know how scientists identify the composition of microbial communities
• Know how various types of sequencing work
• Have an appreciation for how bioinformatics is necessary to evaluate data from large, complex datasets as it applies to many different fields
• Use bioinformatics to evaluate the composition of microbial communities

Prerequisites: Students will need to have taken biology courses that have covered molecular genetics (DNA/RNA, gene expression and regulation). Knowledge of the microbiome is helpful, and is recommended to have taken the “Me, Myself and My Microbiome” Summer@Brown course. Experience using a computer is necessary though experience coding is not needed.


Course Information

  • Course Code: CECS0916
  • Length: 2 weeks

Program Information


Brown’s Pre-College Program in the liberal arts and sciences, offering over 200 non-credit courses, one- to four-weeks long, taught on Brown’s campus. For students completing grades 9-12 by June 2019.

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